The PXDataset to find and download proteomics data

Source: R/px.R

The rpx package provides the infrastructure to access, store and retrieve information for ProteomeXchange (PX) data sets. This can be achieved with PXDataset objects can be created with the PXDataset() constructor that takes the unique ProteomeXchange project identifier as input.

The PXDataset class is replaced by PXDataset2 and is now deprecated. It will be defunct in the next release.

# S4 method for PXDataset
pxid(object)

# S4 method for PXDataset
pxurl(object)

# S4 method for PXDataset
pxtax(object)

# S4 method for PXDataset
pxref(object)

# S4 method for PXDataset
pxfiles(object)

# S4 method for PXDataset
pxget(object, list, cache = rpxCache())

# S4 method for PXDataset
pxCacheInfo(object, cache = rpxCache())

PXDataset1(id, cache = rpxCache())

Arguments

object

An instance of class PXDataset, as created by PXDataset().

list

character(), numeric() or logical() defining the project files to be downloaded. This list of files can retrieved with pxfiles().

cache

Object of class BiocFileCache. Default is to use the central rpx cache returned by rpxCache(), but users can use their own cache. See rpxCache() for details.

id

character(1) containing a valid ProteomeXchange identifier.

Value

The PXDataset() constructor returns a cached PXDataset

object. It thus also modifies the cache used to projet caching, as defined by the cache argument.

Details

Since version 1.99.1, rpx uses the Bioconductor BiocFileCache package to automatically cache all downloaded ProteomeXchange files. When a file is downloaded for the first time, it is added to the cache. When already available, the file path to the cached file is directly returned. The central rpx package chache, object of class BiocFileCache, is returned by rpxCache(). Users can also provide their own cache object instead of using the default central cache to pxget().

Since 2.1.1, PXDataset instances are also cached using the same mechanism as project files. Each PXDataset instance also stored the project file names, the reference, taxonomy of the sample and the project URL (see slot cache) instead of accessing these every time they are needed to reduce remote access and reliance on a stable internet connection. As for files, the default cache is as returned by rpxCache(), but users can pass their own BiocFileCache objects.

For more details on how to manage the cache (for example if some files need to be deleted), please refer to the BiocFileCache package vignette and documentation. See also rpxCache() for additional details.

Slots

id

character(1) containing the dataset's unique ProteomeXchange identifier, as used to create the object.

formatVersion

character(1) storing the version of the ProteomeXchange schema. Schema versions 1.0, 1.1 and 1.2 are supported (see https://code.google.com/p/proteomexchange/source/browse/schema/).

cache

list() storing the available files (element pxfiles), the reference associated with the data set (pxref), the taxonomy of the sample (pxtax) and the datasets' ProteomeXchange URL (pxurl). These are returned by the respective accessors. It also stores the path to the cache it is stored in (element cachepath).

Data

XMLNode storing the ProteomeXchange description as XML node tree.

Accessors

  • pxfiles(object) returns the project file names.

  • pxget(object, list, cache): if the file(s) in list have never been requested, pxget() downloads the files from the ProteomeXchange repository, caches them in cache and returns their path. If the files have previously been downloaded and are available in cache, their path is directly returned.

    If list is missing, the file to be downloaded can be selected from a menu. If list = "all", all files are downloaded. The file names, as returned by pxfiles() can also be used. Alternatively, a logical or numeric index can be used.

    The argument cache can be passed to define the path to the cache. The default cache is the packages' default as returned by rpxCache().

  • pxtax(object): returns the taxonomic name of object.

  • pxurl(object): returns the base url on the ProteomeXchange server where the project files reside.

  • pxCacheInfo(object, cache): prints and invisibly returns object's caching information from cache(default isrpxCache()`). The return value is a named vector of length two containing the resourne identifier and the cache location.

References

Vizcaino J.A. et al. 'ProteomeXchange: globally co-ordinated proteomics data submission and dissemination', Nature Biotechnology 2014, 32, 223 -- 226, doi:10.1038/nbt.2839.

Source repository for the ProteomeXchange project: https://code.google.com/p/proteomexchange/

Author

Laurent Gatto